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. 2019 Nov 11;20:231. doi: 10.1186/s13059-019-1849-2

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 5 — Best practice for analysis of PDM sequencing. A robust workflow to analyze human genome data contaminated by mouse genome. ConcatRef, Disambiguate, and XenofilteR are the best suggested filtering method for general purpose. Alternatively, Xenome, XenofilteR, and ConcatRef are also recommended for SNV analysis. After applying a filtering method, further filtering can be optionally achieved by blacklisting using HAMA list. Estimation of contamination ratio can be used as an indicator of whether strict or lenient blacklisting should be applied